Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Gene expression profilling of day 30 cerebral organoids at the single cell level

ABSTRACT: To characterize cerebral organoids generated using STEMdiff Dorsal Forebrain Organoid Differentiation Kit were flash frozen on Day 30, we performed single cell RNA sequencing

ORGANISM(S): Homo sapiens

PROVIDER: GSE280812 | GEO | 2024/12/19

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Single-Cell RNA Sequencing Analysis of Human Embryonic Stem Cell-Derived Neural Organoids

Project description:Human pluripotent stem cell-derived 3D neural organoids have been shown to recapitulate the major features and cytoarchitecture of early human brain development. We used three commercially available kits: STEMdiff™ Cerebral Organoid Kit, STEMdiff™ Dorsal Forebrain Organoid Differentiation Kit, and STEMdiff™ Ventral Forebrain Organoid Differentiation Kit. These neural organoids contain unique and diverse cell types which model the early brain and are patterned with developmental cues. Here, we sought to investigate the cellular diversity of these organoids using single-cell RNA sequencing.

2023-02-23 | GSE218457 | GEO

Gene expression profilling of day 30 cerebral organoids at the single cell level

Project description:Gene expression profilling of day 30 cerebral organoids at the single cell level

| PRJNA1180579 | ENA

Gene expression profilling of NEUROG2-mCherry lineage in cerebral organoids

Project description:To identify and purify NEUROG2-expressing cells and trace their short-term lineage, we engineered two NEUROG2-mCherry knock-in human embryonic stem cell (hESC) lines. Transcriptomic profiling of NEUROG2:mCherry knock-in hESC-derived cerebral organoids revealed an enrichment of neurogenic, oligodendrocyte precursor cell and extracellular matrix-associated gene transcripts in mCherry-high cells. Conversely, only neurogenic gene transcripts were enriched in mCherry-high cells from Neurog2:mCherry knock-in mouse cortices.

2024-12-19 | GSE277092 | GEO

Brain organoids reproducibly generate the cellular diversity of the human cerebral cortex

Project description:Stem cell-derived human brain organoids hold an unprecedented degree of promise as experimental models of the human brain. They are, however, plagued by poor reproducibility and high organoid-to-organoid variability. Here, we show that a human organoid model pre-patterned to form the dorsal forebrain and cultured for over six months can achieve reproducible generation of a rich diversity of cell types appropriate for the human cerebral cortex. Using single-cell RNA-sequencing of 166,242 cells isolated from 21 individual organoids, we find that 95% of the organoids generated a virtually indistinguishable compendium of cell types, through the same temporal trajectories, and with organoid-to-organoid variability that is comparable to that of individual endogenous brains. The data demonstrate that reproducible development of complex central nervous system (CNS) cellular diversity does not require the context of the embryo, and that establishment of terminal cell identity is a highly constrained process that can emerge from diverse stem cell origins and growth environments.

2019-06-05 | GSE129519 | GEO

Gene expression profilling of NEUROG2-mCherry lineage in cerebral organoids

Project description:Gene expression profilling of NEUROG2-mCherry lineage in cerebral organoids

| PRJNA1160714 | ENA

Expression data from cerebral tumors of WHO grade II and III

Project description:Molecular profiling of cerebral gliomas distinguishes biologically distinct tumor groups and provides prognostically relevant information beyond histological classification and IDH1/2 mutation status. We performed microarray-based genome- and transcriptome-wide molecular profiling of primary tumor samples from 137 patients with cerebral gliomas, 61 WHO grade II and 76 WHO grade III tumors. For this study, we screened prospectively recruited patients with a histopathological reference diagnosis of cerebral tumors of WHO grade II and III, known KPS at diagnosis, information on extent of resection by early postoperative neuroimaging, available frozen tissue specimens from the initial operation, and documented clinical outcome.

2015-04-30 | E-GEOD-61374 | biostudies-arrayexpress

Transcription profiling of different regions of E16.5 mouse cerebral cortex to identify region- and layer-specific genes.

Project description:The mammalian neocortex develops layer organizations with regional differences represented by expression of multiple genes at embryonic stages. These genes could play important roles in the formation of areal cyto-architecture, yet, the number of genes identified so far is not sufficient to explain such intricate processes. Here we collected five regions; the medial, dorsal, lateral, rostral, and occipital, from the dissected E16.5 mouse cerebral cortex and performed extensive gene expression analysis using the Affymetrix U74Av2 array. Keywords = mouse Keywords = cortex Keywords = development Keywords = regional Keywords = gene expression Keywords = medial Keywords = dorsal Keywords = lateral Keywords = rostral Keywords = occipital

2007-12-13 | E-GEOD-929 | biostudies-arrayexpress

Reactive Oxygen Species Mediate Transcriptional Responses to Dopamine and Cocaine in Human Cerebral Organoids [Rudibaugh2023]

Project description:Dopamine signaling in the adult ventral forebrain regulates behavior, stress response, and memory formation and in neurodevelopment regulates neural differentiation and cell migration. Excessive dopamine levels including due to cocaine use both in utero and in adults could lead to long-term adverse consequences. The mechanisms underlying both homeostatic and pathological changes remain unclear, partly due to the diverse cellular responses elicited by dopamine and the reliance on animal models that exhibit species-specific differences in dopamine signaling. To address these limitations, 3-D cerebral organoids have emerged as human-derived models, recapitulating salient features of human cell signaling and neurodevelopment. Organoids have demonstrated responsiveness to external stimuli, including substances of abuse, making them valuable investigative models. In this study we utilize the Xiang-Tanaka ventral forebrain organoid model and characterize their response to acute and chronic dopamine or cocaine exposure. The findings revealed a robust immune response, novel response pathways, and a potential critical role for reactive oxygen species (ROS) in the developing ventral forebrain. These results highlight the potential of cerebral organoids as in vitro human models for studying complex biological processes in the brain.

2023-08-07 | GSE234767 | GEO

Reactive Oxygen Species Mediate Transcriptional Responses to Dopamine and Cocaine in Human Cerebral Organoids [Rudibaugh2022]

2023-08-07 | GSE234766 | GEO

Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation

Project description:Analysis of chromatin accessibility can reveal transcriptional regulatory sequences, but heterogeneity of primary tissues poses a significant challenge in mapping the precise chromatin landscape in specific cell types. Here we report single-nucleus ATAC-seq, a combinatorial barcoding-assisted single-cell assay for transposase-accessible chromatin that is optimized for use on flash-frozen primary tissue samples. We apply this technique on the mouse forebrain through eight developmental stages. Through analysis of more than 15,000 nuclei, we identify 20 distinct cell populations corresponding to major neuronal and non-neuronal cell types. We further define cell-type-specific transcriptional regulatory sequences, infer potential master transcriptional regulators and delineate developmental changes in forebrain cellular composition. Our results provide insight into the molecular and cellular dynamics that underlie forebrain development in the mouse and establish technical and analytical frameworks that are broadly applicable to other heterogeneous tissues.

2018-01-27 | GSE100033 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data